Hello Again, Brother
by Amelia Loves Anime
Summary: The Doctor gets a sudden phone call from Amy. Apparently a Timelord ship survived the Time War, and his 'sister' is the captain. Who is this girl who calls herself his 'sister? How does she know so much about the Doctor and his companions? How did they survive the Time War? Minor spoilers up to the episode 'The Wedding of River Song'.
1. Chapter 1 : The Timelord

Chapter 1

The Time Lord's Archives

* * *

**Authors Note: **

**Hello! This is my first Doctor Who story, ever! As well as the first story I posted on here. I REALLY hope you enjoy it! I'm most definitely having fun writing it. XD Anyway, I'm not entirely sure how everything works, so forgive me if I do anything horribly wrong. The story is set before the 11th Doctor regenerates (that's because #1, I started this story before he died, and 2nd, he's my favorite Doctor!) but it has Clara... (I don't like Clara that much, so I must have started this story before I knew that.. Honestly, I remember writing this but I have no idea when I did... XJ) Things happen, and there just might be a lot of running involved! Disclaimer: I don't own Doctor Who (sadly, are else the 11th Doctor would NOT have DIED from OLD AGE! It's is timelord biology, not a lie! The town he was in that made everyone tell the truth would NOT change how he aged! I hated how he died.)  
**

* * *

As she opened her eyes she saw seven figures standing above her. Her vision was foggy and she couldn't see their faces. She felt very sleepy, but also like she'd been asleep a long time, like she needed to wake up. Suddenly she went totally weightless and her vision cleared. Standing in front of her was a 2 guys, 4 girls and her brother; the Doctor.

One month before…

"Xhvhfiuhvuitiyojxxxxxbgudfddbslghgodgnnlkabuewteithohqbhgvgjciobvdhjl,jfxdsydskfajf" The TV garbled. All the TVs in the house frizzled out for a second...Amy couldn't figure out why, she'd just sat down to watch a movie with Rory when this just happened! Suddenly a clear image came on the screen.

"Amy!" Rory yelled. "Are you seeing this?"

"Yeah!" She yelled back.

On the screen, she saw a man, there was something about him though…Something that reminded her of the Doctor.

"Could everybody stop yelling for a minute, I can hear you just fine." the man said as hundreds of voices broad cast over the TV.

It got quieter and the man began to explain. "You are all acquaintances or friends of the Time Lord known as the Doctor. We need to get in touch with him. He may be the only person who can tell us what happened to our home planet, and save our ship's captain. In the mean time though, we need a place on earth to land our ship. We're almost out of fuel and when we run out it'd be better if we were on a planet, we don't want to crash and we do need life support."

There was silence for a few seconds, then a different man spoke. " This is captain Jack Harkness of Torchwood. We have an area where you can land, but first I'd like to know your species and any problems aboard your ship other than low fuel."

"We are Timelords, but we did bring some Galifrian animals. Our ship was slightly damaged by a Mega Star's time stream ending, but we'll survive for now."

Silence…

"Are you from before the Time War?" Jack asked.

"What time War?" The man asked, clearly puzzled. "We were told that we were going to be test subjects for some sort of test that help with defense from the Daleks. They told us that if it worked than after flying around a little to make sure it was successful, they'd get us out. They never came back. We were lucky, most of us got out of the Time lock they put us in when our ship was damaged. They decided that they'd make one of us the ship's captain, in reserve of course, in case anything happened, but our emergency captain is still frozen. Can't get her out. Without her we can't efficiently pilot the ship, she has the codes."

"I'm sending you the coordinates for the landing zone." Jack said. "Try to hide your ship."

"Thank you."

"What's your name?" Amy asked.

"Professor." The man said. "People call me The Professor"

"Just out of curiosity, what's the name of your ship?" A woman asked. " Oh, and by the way I'm Martha."

"Our ship is named The Archives, and its nice to meet you Martha."

"How did that mega star's explosion even touch your ship?"

"The ship wasn't built for safe traveling, it was built to test something. And it didn't help that someone left the shields down. They never expected us to be any where close to the star. As it is, we're lucky we're still breathing."

"You keep referring to a 'they'; who are these 'they' people?" Rory asked.

"The high counsel; well, I suppose you won't know what that was…The timelord version of a government."

"I can tell you what happened to your people." A woman whispered over the TV.

"Please tell me. But first tell me your name."

"My name is Sarah Jane Smith. The Doctor recently told me what happened…"

"Sarah, let the doctor explain when he gets here, the Professor may take it easier and the Doctor will want to tell him." Another woman interjected.

Amy recognized her voice immediately; it was her daughter, River Song.

"Perhaps you are right." Sarah replied. "The boy is probably worried enough already."

"Please tell me ma'am! I need to know what happened!" The Professor exclaimed.

"Yes, you do need to know, but not from me." Sarah told him.

"Any way, lets get the Doctor and then we can continue this conversation." Amy Said.

"Fine." The Professor said, obviously upset.


	2. Chapter 2 : The Doctor's Family

Chapter 2

The Doctor's Family

* * *

The Doctor raced around the TARDIS trying to make out what was going on. The hundreds of signals trying to get his attention. This was kind of unusual; it was normal in the TARDIS for there be a lot of signals going off, but not like this, not so many of them at the same time. It didn't make sense and there was something happening that the Doctor needed to know. Finally Clara just picked up the phone.

"Hello?"

"Finally! You know raggedy man, you can be a very hard man to get a hold of. Probably all that running around you do! Come to Torchwood as soon as you can. I know your probably busy eating fish fingers and custard or something, but it's important. And you really should answer your phone more." A woman spoke from the other side of the line with a very Scottish accent, before hanging up.

"Doctor? Who was that?" Clara asked.

The Doctor didn't answer for a few seconds as he ran around flipping switches and muttering to himself. Once they had landed he finally answered. "Amy is an old friend of mine, she wouldn't have called if it wasn't important… Come on."

And with that he ran out of the TARDIS, and of course, Clara followed him. Outside the TARDIS stood about a hundred people, and the Doctor seemed to recognize all of them. He took a step back in amazement, but Clara just stared, she knew none of the them. Amy was the first one to hug him, but there were many hugs to follow, and even some tears.

"How are all of you here? This is impossible! Some of you were in different time streams, how can you all be here at the same time as each other?"

"You gave us a lift yourself, but you said your younger self had to be the one that helped us." Explained Rory.

"Because it couldn't not happen, this is a fixed point in time." River continued, smiling. "Hello Sweetie." She said with a kiss to the cheek of her husband.

"Why did you call?" Clara asked.

"Why did we call? We found something; a Galifrian ship, and there are survivors. May I ask too, who are you?" A teenage girl with silky blonde hair in a high pony tail said, the last question direct to Clara, the girl obviously already knew the Doctor.

"Jenny! You're alive!" The Doctor exclaimed.

"I am your daughter am I not?" She said laughing, and hugging her father said, "Good to see you, though, you have changed your face on me."

"I'm, Clara Oswald. I'm guessing you're Jenny." Clara told Jenny. "Frankly though, I didn't know the Doctor was a father… he doesn't really seem the type…"

Jenny laughed. " I'm kind of the product of a machine, the Doctor is both my Dad, and my Mum. Came out fully grown two minutes later with knowledge of what was going on around me, and, how to fight. Weird huh?"

"Really!" Clara said in agreement.

"What's this about a Galifrian ship?" The Doctor asked.

"A month ago a ship signaled us, turns out they are from Galifrey and they are from before the time war. They didn't even know about it. We figured you'd want to tell them so they still don't know what happened. Oh, and you'll want to meet their ships captain, sweetie." Explained River to the Doctor.

"How am I a month off?" Protested the Doctor.

"Oh, you don't answer the phone much. I told you that when I called." Amy said.

The Doctor smiled. "Well, lets go! Come along Ponds! Clara, lets go see this ship!"

Captain Jack led Clara and the Doctor to the ship, and into Torchwood. They went down in small groups, the elevator only holding so many at a time. In their group it was the Doctor, Clara, Amy, Rory, Jenny, River, and Jack. Everyone else trailed a little bit behind, interacting with the Timelords they grown to know in the month the Doctor was late that were waiting for them above Torchwood. The entrance was a concrete slab in the sidewalk by a fountain. Clara watched as the slab under her feet lowered into a large room with numerous computers and consoles, and of course, LOTS of blinking lights. They came down on the right side of a column of wires that went to the very top of the high ceiling. Above her head there seemed to be a pterodactyl flying around.

In front of her once they had reached the bottom, was a single door standing on its own, with nothing behind it. The Doctor stepped off the platform and opened the door, the door that led to a entirely different part of space…

They walked in and there seemed to be millions of time Lords watching them, and there probably was. A man walked up to them. He had dark, black hair and blueish hazel eyes. His skin looked a tanish white. He looked to be in his late 40's but Clara knew he could be as old as 3,678 or older, as Timelords don't age like humans.

"You must be the Doctor. I'm The Professor, I've heard a lot about you. You're the captains brother. Though you probably already know that she's the captain, so I suppose that sentence was just a waste of time. My apologies." The Professor said in a kind of rush.

"I've yet to see her. I don't remember having a sister. This is new to me, having a sister." The Doctor said almost giddily, but also questioning the Professor's statement.

"Follow me." The Professor said.

"Where?" The Doctor asked.

"The Catacombs. You'll see."

* * *

It took a little while to get to the catacombs, but once they got there Clara couldn't help but to be amazed. Six foot metal pods lined the walls, each with a small window so you could see a persons face inside. There seemed to be millions of them. They were shaped almost like pills, but they had people in them, and some of the people were climbing out. Clara understood now why they were called the catacombs, it was because the room seemed to be carved out of a cave, and a huge one at that.

"Oh, that's clever! That's very clever! You stopped the flow time in a isolated space! Wired it so the ionic energy flowed outside the space as a kind of barrier! Protecting it from the stray disruption of the time stream, mind you, you must have been hit pretty hard to disrupt that thing and get out of the freeze. That's very good! Never thought of that before!" The Doctor exclaimed, running over and studying one of the pods.

"Why thank you Doctor. But not exactly the reason we asked you here. Come along, the captain's been waiting long enough. It 's about time we figured out how to get her out too." The Professor said.

"You mean my sister." the Doctor said, turning more serious before getting giddy again, bouncing on his heels. "Well, let's go!"'

The Professor lead them down several corridors, and into a room with a single pod in the middle, no windows like the other had, just a solid door with a collections of buttons instead of a door handle. Clara reached out towards it only to feel a invisible wall in the way.

"Ahhh," The Doctor whispered as he to reached out to feel the wall. "You can't even get close enough to that capsule to even begin to unlock the time freeze. Your ship was sent into emergency mode, sent the majority of its remaining power sealing this and from the looks of it, a few other capsules, off from the rest of reality. Really, that's rather brilliant, but in this case, a rather big problem. I do have one question though, one rather important question. Why did you call for me? Why didn't you call the High Council first? I mean they're the ones you said were running this ship. Even if I was the Captain's brother, you'd still call the High Council. Why me?"

"I-I, I'm not sure… why did I do that? Doctor? Why would we do that?" The Professor asked, highly confused.

"I don't know yet, but I'm working on it. There seems to be a weakening psychic signal coming from your Captains capsule. Maybe we should ask her next time we get the chance."

"Yes, but how can we do that? You said yourself the Ionic energy is keeping us from even getting close enough to get her out. What's your plan?"

"Don't have one yet. Haven't stopped talking. So, what can you tell me about my 'sister'?"

"Only that she's a mystery. She's one of the youngest Timelords here, only 178 years old. And yet she's the Captain of the ship and the High Council seemed to trust her with quite a lot of information. I've never seen anything like it. I heard rumors she is the one who designed and built this ship. Even convinced the High Council to go along with it after only talking to them once in her entire life. Never been off of Galifrey before now, never even regenerated yet. She's the biggest mystery I think I've ever seen; and let me tell you, I've seen more than my share of impossible things. The one time I spoke with her she knew things she never should've even heard about. I don't even feign understanding her and I'm pretty sure she knows it. You don't even know about her, and you're her brother. Like I said, she's one big puzzle."

"Hmmmmm, that is interesting. Now I _really_ want to have a talk with this 'sister' of mine." The Doctor's voice practically dripping with giddiness, and there was a brilliant gleam in his eyes. Trust the Doctor to get this excited over any hint of a mystery.

"But Doctor, how are we supposed to do that? It's not like we can just talk to her. There's this wall thingy in the way!" Amelia questioned the giddy man she waited for, ever since he crashed into her yard when she was seven, to see the universe.

"Oh mommy dear, no wall stands a chance against that man when he's curious of whatever is on the other side of it!" River laughed.

The Doctor smirked, and his thumbs pulled at his suspenders, proud of that little fact. With a snap, his suspenders popped back into place and he clapped his hands together.

"Right! River, go to the TARDIS, get the isokinetic extrapolator, an electromagnetic inductor coupling, a neutrino inversion castalator, an antimatter inversion generator, a foot of twine, a half chewed stick of bubble gum, twenty jammie dodgers, and a fez!"

" 'course Sweetie." River said as she ran off.

"And don't shoot my fez!" The Doctor called after her, to which she didn't answer.

"Okay, let's get started!" The Doctor said as he went over to a panel in the wall, pulling out wires, disconnecting some and connecting others.

Deciding this may take a while, the Doctor's companions started to exchange stories of their adventures with the Doctor and their lives on Earth. Amy was just telling them the story of the year the Doctor spent domestic, the slow invasion, when River came running back in. The Doctor looked up for the first time since he had opened the panel and took the gadgets out of River's arms.

"Where's my Fez?"

"I shot it."

"What! Why?" The Doctor pouted. River just laughed at him.

"Because Fez's aren't cool! Doctor, how many times do we have to tell ya?" Amy answered for her.

"Oi! Fez's are cool! It's why I wear a Fez now!"

Amy just gave him a pointed glare.

"Fine. You win,_ for now._ River, come over and help me with this." The doctor said while moving his hands like he was shooing the topic away.

"What are we doing?" River said walking over to take a look at the panel the Doctor had been toying with.

"Were prying the wall down. Rerouting the energy to our TARDIS so the ship doesn't have the power to keep the wall up."

"Oh! That's brilliant!"

"River, you have that face again." the Doctor said smugly.

"What face?"

"The 'He's hot when he's clever' face."

"This is my normal face!"

"Yes it is." His smirk grew ever larger.

"Shut up."

"Not a chance."

"Um? Aren't you going to take the wall down?" The Professor said, feeling slightly out of place in the midst of the Doctor's flirting.

"Oh, don't worry, handsome. The Doctor won't do anything too naughty. Now me? Well, let's see about that…" Jack laughed as he leaned against the invisible wall, trying to act all cool. The Professor had a look of complete shock plastered to his face.

"Hhmm? Oh! Right! Rerouting energy… Now!" The Doctor said after getting his head out of the clouds, connecting two wires as he said it. As he did the wall came down, and Jack fell on his butt.

"Hey!" Jack exclaimed.

"That's what you get for flirting instead of paying attention!" They Doctor replied, laughing as Jack rubbed his now sore buttocks.

"Cough, cough, hypocrite, cough, cough" Amy whispered, laughing with the others from the corner of the group.

A loud click, made the group of friends drop their conversation and turn to the pod holding the Doctor's sister. As the door opened, the Doctor took several steps towards the young Timelord at the brink of waking. The girl was weightless for a minute as she gasped and her eyes flickered open before gravity took its effect. She stumbled forward before leaning against the pods door as she caught her breath. The girl had short blonde hair, young, bright green eyes, and tanish skin. She wore a light, almost white, blue dress, that was done a Greek style, complete with leather sandals.

"Finally!" The girl said as she caught her breath. "I was beginning to wonder how long you were going to take Brother. Or would you rather I call you Doctor? What about John Smith? Sir Doctor of TARDIS? Spartacus? Zeus? Great Wizard Qui Quae Quod? Captain Grumpy? The Watcher? The Caretaker? The Examiner? The King of Okay? The Great Exterminator? Spaceman? Matchstick Man? Chin Boy? Madman? Madman In a Box? Raggedy Man? Raggedy Doctor? Sweetie? Thief? Bringer of Darkness? The Oncoming Storm?… Theta Stigma? So many titles, nicknames, names. Always running away." She gasped and a golden light floated out of her mouth.

"But who am I to tell you that?" She said as she watched it. "In a way, I'm running too. Running from the future, the war. Yes, maybe we should keep running." She looked past the Doctor and saw his companions gaping at her. "Oh! I see brought friends! Humans…Mostly." She looked directly to River. " This one's a bit complicated isn't she? Oh, I love complicated things!" Her attention turned to Jack. "And you, you're an anomaly. You should be dead, but you're not… Badwolf? What does your living have to do with Badwolf?" Again her focus wavered, this time landing on Jenny. "And you,,, Brother dear, I knew you were a father, but I never knew about this one. Oh, but who was the mo-? Oh! Oooohhh! Brother! I didn't know you were a narcissist!" She said with a laugh and a smirk. Her attention finally fell back to her brother. His expression had turned worried since she let the light escape her lips.

"Ahh , how humans intrigue me! They're so normal! And yet, so extraordinary! Never could figure them out. And that's saying something, 'cause I'm quite brilliant. Oh, and the stories I've heard of you, Brother dear. So many adventures. You've seen, so very much. How I yearn for that. In many ways you're lucky Brother. But in many others you've had a very hard life, haven't you?" She gasped for air, and her skin began to glow.

"Oh, would you look at that, I'm dying. Well, I directed the energy of the Mega stars explosion in here so it wouldn't destroy the ship. I don't suppose anyone could survive that." She coughed violently, cringing. " Oh, this is no fun, dying. I'll have to remember that. No more dying for me… Hopefully." She let out of shriek of pain, and the Doctor tried to step forward to help, but the girl just waved him back. " Goodbye, Brother.." As those gentle words quietly passed her lips, everyone was forced to take a step back and shield their eyes as the girl in front of them burst with regeneration energy for the first time in her life.

* * *

**Hey Everyone! Maddie here! Hope you like the story! It's getting started really and I'm not exactly sure where it's going, so, if you have any suggestions, please leave a review with your ideas! I have a few ideas already but I'll be very happy to get you guys' support! Thank you again! Much love!  
**


	3. Chapter 3 : A Brand New Sister

Chapter 3

A Brand New Sister

* * *

The light faded and a completely different woman tumbled forward only to pass out in the Doctor's arms. A whispered name passed her lips.

"Doctor…."

The woman had should blade length, fiery red, wavy hair. Her skin was paler, and there was only one freckle that touched her face, on the right corner of her mouth. Her eyes had only looked golden before she closed them as she entered a state of unconsciousness, but they all got the feeling, her eyes had change colors. Her figure was slightly more curvy than before, and she looked a little older, but still rather young, like she was in her late twenty's compared to maybe the twenty-one she looked before. Rory's nurse instincts kicked in and he ran over to her, trying to make she was alright.

"Is she okay?!" He worriedly asked the Doctor.

"She'll be fine. A good cup of tea would be a good idea though. Super heated infusion of free radicals and tannin, just the thing for healing the synapses." The Doctor nodded.

"Right" Rory said, obviously the things the Doctor had just said meaning nothing to him, he turned to the Professor. "Can you make a cup of tea?" the Professor nodded, and ran out of the room. Clara finally got over her shock.

"Doctor, what the _hell _just happened? How did she turn into a different person?!"

"Oh, that's right, you don't know…" The Doctor said just giving her a blank look, like he had expected her to just know. River decided her husband wasn't going to answer the clueless girls question, and picked up the slack.

"She regenerated, it's Timelord biology. When the are dying, their bodies trick death. Their bodies die, but they basically grow another one. They keep their memories though. They don't forget their past lives."

"So, you're telling me they die, and came back to life?" Clara's expression showed that she halfway believed it, but her brain just wanted to tell her it was ridiculous.

"Basically, yes." River again answered not even blinking. Clara just gaped at her.

"Has the Doctor regenerated? I mean surely he hasn't- has he?"

"I've regenerated twelve times now." The Doctor whispered, still looking at his sister.

"What?! But How-?"

"Different ways. It doesn't mean anything though, I'm still the same man. Different face, different opinions on some things, but I'm still the same man. I've always followed my current principles. Just ask Sarah Jane, she's known several of my regenerations. She knows, I'm the same man I was then, just- slightly different."

"…Okay." She said, finally excepting the truth, but the shocked expression did not leave her face.

A moment of silence passed before the Professor came back into the room carrying a cup of steaming tea. Quickly he handed it to the Doctor. The Doctor nodded thanks before turning back to the girl in his arms he had lowered to the ground.

With one hand he waved the drink under her nose and with the other he supported her head. After a few seconds her head turned towards the tea, her eyes still closed, and she took a deep breathe. Slowly her eyes fluttered open. Now they could clearly see, her eyes had indeed changed colors. Now they were a brilliant crystal blue, with hints of bright green near her pupils. Her eyes frantically danced around trying to figure out what was going on.

"Where-? Where am I? I don't remem-" She paused, her eyes finding the Doctor's. " Oh, did I-?" She looked down at her hands flipping them so she could see her palms and the backs of her hands, taking in every detail, as she sat up, out of the Doctor's grip.. She grabbed at her hair, trying to figure out what she looked like now.

"My fingers, are longer, and, am I ginger?! I've always wanted to be ginger! Oooh! And my hair's longer! Curlier!"

"Why does my sister get to be ginger and I don't? I always wanted to be ginger!" the Doctor pouted and River giggled, thinking he was adorable when he pouted like that.

If the full female Timelord heard the Doctor's muttering, she didn't act like it. Her hands ran down her figure, tracing it, as she stood. " This body has some curves now doesn't it? Oh that is nice! Wonder if I was trying to show off?" She laughed at that. "Oh well! I like this body!" Her voice was different too, light and sing-songy now, whereas it had been richer before. Like the difference between that girl in that band, 'Florence and the Machine' vs. Regina Spektor's voices, Amy thought. (A/N: Look them up if you haven't heard them, they're good! Love 'em!)

Finally she seemed to notice the others in the room.

"Aahhh, you'll want answers for everything I said earlier won't you?" She asked warily. She seemed to take their silence as a yes and sighed.

"Great, just leave it to me to let out too many secrets when I die. Well, where should I even begin?" Then she scrutinized every face in the room, her brow furrowed. "No, wait, it's too early to tell you everything…. You have to lack the knowledge a little while longer. I'm sorry, but it's not the right time right now. You can ask one question, but depending on what it is I might or might not be able to answer properly." Everyone in the room was sent reeling for a question to ask when finally Amy asked one.

"What's your name?" She blinked realizing her in mistake, Timelords don't just give you their name. "I mean, what do I call you?" The Timelord in question blinked at her, and then burst out laughing.

"Oi! Why are you laughing?! It wasn't a horrible question!"

"No! It's a fantastic question!" The woman said, stifling her laughter. "It's just, you could've asked me anything, and all you ask is what my name is! This is why I love humans! They think of some of the most out of the box stuff. It really is a brilliant question though. I can't tell you anything I shouldn't while answering it! But it gives me the potential to answer many more questions, and you'd also know who I am! Well in a sense anyway." Finally the woman got her laughter in order and actually thought about the question and answered it.

"Call me… I suppose Adept works? Yes, I rather like that. Call me Adept."

"Adept…" The Doctor whispered, like he was trying out the word. "Adept… I suits you… somehow." He said louder, making sure she heard his words. Adept gave him a soft smile and her eyes sparkled, happy that her brother approved of her new name.

"Glad you approve. Though I must say after all the stories I've heard about you, I kind'a pictured you differently" She said a glint a mischief surfacing in her eyes, a smirk tugging at her lips.

"Oi! There's nothing wrong with this face!"

"Nope!" She said laughing at her brother.

Then Clara realized something, this woman they had just met, and had just met them, was letting them read her emotions as easily as a person breathes. It seemed very clear to Clara too, that if this woman didn't want them to know, she could very easily hide her feelings. She was just that type of person. And yet she didn't hide anything from them, well aside from what she couldn't tell them. She had put a great deal of trust into people she'd just met, to just let them read her like this.

"Why are you trusting us like this?" She asked, and everyone turned to her with a puzzled expression trying to figure out what she meant by that. "I mean, you're just laying out your emotions before us, when it seems to me, you could easily hide them. You just met us and you're letting us read your emotions like a open book. Why?"

Adept just laughed again. "Oh, it's rather simple. Whereas I might not have met my brother before, I know him very well. And I know, anyone who he travels with has to be a certain type of person. A very trustworthy one. I know I can trust everyone in this room. Even the Professor, who I can't be as sure about, I know his story well enough, I known I can trust him well enough too. Do you find that strange?"

"Well, yeah. It's not normal for someone who just met you to let you actually see them as they really are. Normally the first thing you see of a person is their shield. Protecting their real thoughts and emotions, it's just how people work. Even children can see that, though a lot of the time when they're younger, they haven't made that wall yet."

"I suppose you are right, but where's the fun in that?" Adept said with a laugh. Suddenly the ship shook violently, throwing them around the room. Finally it stopped and everyone slowly crawled to their feet.

"What the hell just happened?" The fiery red head with a Scottish accent said through gritted teeth.

"Not sure. Is everyone alright?" The Doctor called out, already on his feet. A mild consensus answered him and he nodded.

"Then let's go figure out what that was!" Adept said excitedly, also on her feet. After her statement she grabbed her brother's wrist and dragged him out the door, not even waiting for the others, but trusting that they'd follow. And with a few groans, they did.

* * *

**Haha! Cliffhanger! Try to figure out what happens next! XD**

**Thank you for reading!**


	4. Chapter 4 : Trouble's Brewing

Chapter 4

Trouble's Brewing

* * *

Adept raced down the corridor in front of them her flaming hair whipping back behind her.

"Which way to the controls?" They Doctor asked, only a step behind his sister. She pointed right as she turned.

"This way!" She called as her gravity suddenly changed and she was running along a corridor in the ceiling. With a few more twists and turns and strange gravity switches, they finally arrived at the control room. As Amy and the rest of the Doctor's companions looked around the room, they couldn't make sense of anything: The only one who looked like she might understand any of it was River. At least twenty Timelords stood around the room before them, running around flipping switches, punching in codes, pressing buttons and all the like. Monitors, buttons and switches where everywhere you looked, not one space in the room empty, even the floor was one giant screen monitoring all the rooms and corridors on the ship. The room wasn't small either, it was about as big as your average school cafeteria.

"What happened?" Adept asked, immediately taking charge of the room. When the Timelords in the room noticed her they all seemed surprised, some calling out 'Ma'am!' as they straightened their posture recognizing her as their superior. Even though she had recently regenerated, they still seemed to recognize her, as if they'd already seen this regeneration.

"We aren't sure exactly, everything was fine and then the ship was hit but what looks like a shock wave, we lost our artificial gravity for a minute before we could fix it. So far I don't think anyone was hurt, but we have yet to receive reports from the whole ship." One of the Timelords stepped forward and spoke. The man looked to be in his mid to late twenties, with brown-red hair that was cut so strands invaded his vision. The man had green eyes, a rather athletic build, and was around 5'8" in height. He wore they same clothes you'd expect to see on your average walk around a park, or for that matter just down a normal, everyday street: he wore a blue t-shirt with what looked like a quote written on it, 'wibbly wobbly, timey wimey… stuff ' (A/n: Hehe! Just had to do it! XD), a gray hoodie, jeans and black high top converse. One thing Amy noticed as she looked at him though, was a gold and silver pocket watch hanging out of his jeans pocket. There appeared to be symbols on it, but she couldn't make them out.

"Good work" The Doctor commented. "What's your name?"

"I'm the Watchmaker." the man replied. "And you are-?"

"I'm the Doctor." The Doctor said with a smile, always happy to introduce himself, as he straightened (his already straight) bow tie. The man gasped, his eyes flickering to Adept, apparently aware of their relationship as siblings, his eyes seemingly asking her if what the Doctor had said was true. She nodded.

"Let's take a look at those readings, see if we can figure out what happened." She said walking over to the controls, flicking a few a screen swung in front of her, a few more and then she began intently studying the screen, the Doctor and River walking over and joining her. After a few minutes of going over the screen, her fingers flying across the buttons in front of her, she froze and gasped. About a minute later the Doctor seemed to realize why.

"no, no, No, NO, NO! But that's impossible! They can't be be here! They shouldn't've been able to move us, much less find us! We were hidden, parked, everything! How'd they even get here? This shouldn't even be possible!" The Doctor went on, taking over the controls from Adept to make sure what he'd just read was indeed correct. Adept just stood there, still frozen with the same expression plastered on her face: shock, with every trace of fear.

"Doctor, calm down.. What's going on? What's wrong?" Amy said because she knew she would never find out what the heck was going on if she didn't ask the Doctor now.

"They're here. They're all here. All of them." The Doctor said, running his hands through his hair rubbing his face like what he does when he's trying to figure out what to do next, as he took a few steps back. Beside him, River who'd still been searching the information for answers, gasped too, the info finally clicking as the Doctor said, "It was a trap."

"What do you mean?" Jack asked with a nervous tone to his voice, as he scanned the room suspiciously, like the Timelords around them were about to attack them. The Doctor seemed to note of it as he frowned and shook his head.

"No Jack, not them! Geez, come on! No-! It's not the people on this ship. It's who let this ship land on Earth, directed it towards Earth, forced it to land."

"Who?" Jenny and Clara asked practically at the same time. But this time it wasn't the Doctor who replied, it was River who answered for him, at the same time telling him she was on the same page he was... and it wasn't a good one.

"Daleks, every last fleet, probably in existence. And they're all right here. When the artificial gravity let out, that was them teleporting us to their ship, and with the ship we're on damaged like it is and since we took even more power away from the ship when we lowered the wall around Adept, our shields were weakened so much that we couldn't stop them. We're trapped on a Dalek ship surrounded on all sides by about 10 billion Daleks."(A/n: while reading this listen to the Doctor Who score: The Daleks. Seriously, it matches the situation perfectly! C; )

"Fucking bloody hell! How'd they know where we were?!" The Watchmaker cursed.

"Probably followed us here. Most likely the noticed us when the ship was repairing itself after the mega star exploded, and used us as a trap for my brother to get him here and then from there, well, they kill two birds with one stone." Adept said, seemingly finally reigning in her astonishment enough to were she could move and speak.

"What the hell are we going to do?" She muttered to herself, but everyone in the room heard, and agreed. They were so very dead if they didn't come up with something. At times like these Jack couldn't help but wonder how the Daleks escaped Bad Wolf, they really shouldn't've been able to. Rose had divided every Daleks' atoms through out time and space and should've been able to see every Dalek in existence in all of time and space, so why couldn't they just **all **be dead?

_'Maybe this was a fixed point in time and she couldn't?'_ The logical side of his brain fought, and he hated the thought, but it was the only explanation he could come up with. Still, it just felt so unfair. He was probably going to die **_a_****_l_**o**_t_** from this.. and even worse, he was probably going to lose way too much today. Everyone else in this room too.

* * *

**A/N: Hey everybody! Sorry I haven't updated in a while, but last week I had three four hour tests in a row for school and after that I just didn't feel like writing anything.. But I'm back to writing now! \~^v^~/**

**I'm not sure how busy I'll be in the future, but I'll at the _very least _update once a month. (Cross my fingers... Waahh! Actually.. I'm really not sure how often I'll be able to update because, you know, life.. but that's what I'll aim for! *determined expression, holds fist in air as if to challenge life to stop me from updating story* Okay, I got this!)**

**(^-^)**

**Have fun you guys! Hope you enjoyed it so far!**


	5. Chapter 5 : Out of the Frying Pan

Chapter 5

Out of the Frying Pan

* * *

As the group stood around in shock of their new found knowledge, the screen on the wall in front of them opened up a comms-link with the Daleks as the Dalek tried to talk to them.

"Where is the Doctor? The Doctor and his relation shall step forward. The Doctor and his relation shall step forward or you will be exterminated!" The Dalek on screen said in it's menacing, robotic voice, it's eye-stalk swinging around as it looked for them. not having much choice, after sharing a glance, the Doctor and Adept stepped forward. Adept immediately started questioning the Dalek.

"What do you want? Why haven't you killed us already? Our shields are down, we're defenseless, you out-number us by billions, but we're not dead." Her gaze grew even more steely than it had already been.

"You want something." This time it wasn't even a question, she said it as a statement."What?"

The Dalek seemed to squirm under her gaze, evening backing up a step before answering. This kind of startled Jack, the only person he knew who could make a Dalek take a step back with only words was the Doctor. Who was this girl? Really?

"The Doctor's relation has knowledge that is useful to us, she shall give us the information we want or you will be exterminated."

As the Dalek said that, looking at Adept, Jack couldn't help but wonder how she would know things the Daleks would want or even how she knew all that stuff about the others and himself. It didn't make sense. Even if she'd met a future version of them, they had no reason to tell her all the things she knew. There were just somethings that she shouldn't know, and he knew at least he wouldn't've been willing to tell her, and he doubted the others would be any more willing to tell her, so how the hell did she know them? As if Adept knew what they were thinking, she lowered her gaze, and glanced around at them, silently saying 'I'll tell you later,' before looking back to the Dalek.

"Well, you're not getting that information. Deal with it. I'm not telling you."

"You will tell us or you will be exterminated!" The Dalek screamed, bristled by her reply.

"No."

"Explain yourself."

"I said 'no'."

"What is the meaning of this negative?"

"It means, 'no'."

"But you will be exterminated!"

"No! 'Cause this is what I'm gonna do. I'm gonna save this ship from the middle of the Dalek fleet, and the I'm going to fly us back down to Earth, and—just to finish off—I'm gonna wipe every last stinking Dalek out of the sky!"

"But you have no weapons, no defenses, no plan."

"Yeah! And doesn't that scare you to death."

At this statement the Dalek visibly reacted, its' eye-stalk swinging as it backed away before the screen went dark.

"Well, that was fun. What to do now. Hhmm. They'll back off for a little while after that last conversation. They'll be trying to figure out what were are planning before they attack. That'll hopefully give us enough time to come up with that plan. Any ideas? Anyone?" Adept said turning around and looking at everyone, but they just looked at her in shock. She'd just threatened 10 billion Daleks, without even the slightest hint of being nervous or scared, and she turned around and told them she had absolutely no plan. She was either a brilliant genius, or a idiot, who was about to get herself, and everybody else, killed.

"We could start by getting the energy the TARDIS took from the ship back, that way we might have enough energy to get some shields up. It'll at least slow them down while we come up with something else." River offered.

"Good idea. River, take the Professor and go get on that in a minute, first we need as many brains as we can get thinking of a actual plan." Adept told her and she nodded and Adept turned back.

"But even with those shields, we'll still need a weapon. We're dead if we don't get one." The Watchmaker reminded Adept, and she nodded, frowning, obviously puzzled over the problem.

"What experiment were you running on this ship?" The Doctor interjected, looking around at the controls, seeing if they would give him a clue as to what they were doing aboard 'The Archives'.

"Why?" Another Timelord asked who had previously stayed silent. This one a woman with brunette hair held in a intricately braided bun, and red robes like you'd see the high council wear. The woman had icy blue eyes, and tan skin. Somehow she carried a air about her that reminded Jack of a Captain, even though the actual captain was much younger, and didn't seem carry much of that air at all, at least that he'd seen so far. Adept carried much more so a air of mystery, one that Jack pondered if would ever leave the girl.

"Because, depending on your answer, we might have ourselves a weapon." The Doctor answered, his eyes never straying from the controls before him.

* * *

**A****/N: Hey everybody! I Know this chapter was kind of short.. but, oh well. Sorry! Anyway i want to to give a special thanks to 33 Vi, and Amy bergset for reviewing! You two (if you're reading this..) really motivated me to hop on to this story and really get to it, (I wrote like two chapters just because seeing these reviews made me so happy.. it's nice to know people are enjoying the story!) Anyway thank you guys for reading! Hopefully the next chapter will be longer..**


	6. Chapter 6 : And Into the Fire

Chapter 6

And into the Fire

* * *

**A/N: Hey guys! Thank you for reading the story so far! I hope you are having as much fun reading as I am writing. Anyway, quick warning, in this chapter, there are a few references to The Day of the Doctor, but I will do my best to keep spoilers out. You really don't have much to worry about, but I know some people haven't seen the movie (and it hasn't been spoiled for them yet), so just in case, heed this warning! (though I'm probably just being paranoid...) Anyway, read, enjoy, review!**

* * *

The Doctor glanced back at his fellow Timelords, his eyes still searching for a answer. Several of them frowned, and they seemed to be looking for the answer themselves. Many looked to Adept, as if they were asking her too, 'What were they doing on this ship?'. Seeing this, the Doctor and his companions eyes steeled their gaze at Adept. Adept was the only one who didn't seem to be struggling for answers. Instead, it seemed to be everyone's gazes that unnerved her.

"Adept?" The Doctor questioned, "What is it you aren't telling us?" Adept eyes dropped to the ground, and she shifted her weight from one foot to another as she tried to find a way to answer.

"The Ship- well- it's hard to explain." Adept eyes suddenly shot up to meet the Doctor's, one emotion prominent in her crystal blue eyes... Realization. "The war.. Doctor, you know as well as I, as children Timelords must look into the time vortex. And I saw it.. I saw the war. I saw many things yet to come and many things of the past. I know of your choice, your actions. But I couldn't figure out which Path you took. Did Galifrey fall or does Galifrey fall no more? I couldn't be sure! So, the ship is as it's name implies, an archives for Galifrey. Plants, animals, cultures, people, technology, it's all here. It's like that tale, the one your humans tell. Joan's arc? No.. Noah's boat? No, that isn't quite right.. Noah's ark! That was it! Bit off track there, wasn't I? Anyway, we couldn't just scare everyone with next nothing to prove it, but the High council agreed with me to be safe, we would build and crew the ship. There are a few experiments being conducted on board to lessen suspicion, but that was never the true purpose of this ship."

To Jenny it felt as if the room had been electrified. Jenny knew there had been a war, and her father had been a soldier, but she couldn't understand how Adept could. Adept was so _young._ It didn't make sense! How did she know all of it? What had she meant when she said she had seen things in the time vortex? It didn't make any sense to her, but it seemed something had clicked for the Doctor and River, for their eyes grew wide and a gasp escaped River's lips.

"So, you're saying, you looked into the Time Vortex, and you didn't run, or go insane, but instead it showed you the same things a TARDIS would see?" the Watchmaker asked still confused, but he seemed to understand. Adept nodded, biting her lip, as if she expected someone to be mad at her or she was guilty of something.

"How is your mind not burning?" Jack's question was whispered and Jenny barely heard it, but Adept obviously did. Her head shot up and her eyes widened for a second, before she quickly recovered and whispered back.

"Sometimes I forget you knew the big Bad Wolf."

Everyone was silent for a beat, contemplating all of what she had just said, when the Doctor finally took his turn to speak.

"Why don't you answer Jack's question?" Adept's eyes turned anyway so they could to avoid the Doctor's and everyone else's eyes in the room; Which was rather difficult seeing as how many people were in the room, but she pulled it off. She reminded Jenny of a guilty teenager: she didn't try to argue, like she was sad with herself, and guilt shone on her face, but she didn't have the panicked look of a child caught red handed; and that seemed answer enough for the rest of them. Her mind _was_ burning. She had just been doing a good job hiding it.

"It hurts doesn't it?" The Doctor asked with a gentle quietness, and with sad eyes. "Why didn't you say anything?"

Even though the doctor had only known his sister for maybe thirty minutes, he seemed to have taken up the role of caring big brother, though this didn't surprise Amy much, she saw him so very often becoming a part of everybody he ever met's family. Still, seeing him interact with his real sister, it was something. They were both genius', and absolutely mad(from what Amy seen of Adept, she thought she qualified as mad at least,) the same tendency to get off track, and they both cared, so much. In fact Amy had no trouble believing that Adept wouldn't even think twice about giving her life to save another, just like her big brother. Amy realized then, just how alike the two really were, and it amazed her. It as like there were two Doctors, minus a rip in the fabric of time and space, because the Doctor can't cross over his own timeline.

"We have other things to worry about. Namely, Daleks. So, we can either worry about my mind incinerating itself, or the rest of our continued existence. I vote for the latter." Adept said, turning back to them with determined eyes after taking a deep breath.

The Doctor frowned at her words, but he didn't argue. He, and everyone else, knew she was right. They had bigger problems. But it didn't change the fact that Adept was dying, and they needed to stop it.

"River, why don't you go ahead with the Professor, we need those shields, and quickly, those Daleks aren't going to stop just so we can have a heart to heart chat. We'll try to come up with something while you do that."

Though her reasons for asking River and the Professor to leave were justified, Amy couldn't help but feel Adept was just trying to pull the attention off herself, and onto the problem at hand -Which was probably a really good thing since the were facing billions of Daleks and probably going to get killed.. But it was like she didn't care that she was dying. She put her own life behind everyone elses, yet another similarity between brother and sister. River and the professor left, but not before River shot a worried look towards the Doctor, and though he seemed oblivious to the look, Amy knew he had seen it. He was just thinking to deeply to give any sign that he had, his normal childishness had disappeared in a blink of an eye.

"So what are we going to do Captain?" The female Timelord Jack had noticed earlier asked.

"Architect, do you think we can use the same technology we used in the Time Pods to trap Daleks as they come in?"

"We might be able to, but there aren't enough pods to trap all of them, it's a temporary solution" The female Timelord- Architect, explained.

"Yes, but it'll give us precious time to come up with a actual solution. Okay, let's do this!"

And with that, Adept ran over to the controls and started rerouting power, and giving orders to the other Timelords around her to go down to the pods and reroute the technology in the pods so they would catch the Daleks as the go past. The Doctor and his companions were helping any where they could. Depending on how fast or slow they got this done, they could live or die. But still, it seemed to Jack, their problems were only growing. The Captain- no, the Doctor's sister was dying, and the were surrounded be billions of Daleks. But one thing had changed, watching Adept as she gave orders, Jack decided, maybe she did have the air of a Captain.


	7. Chapter 7 : I'm so Sorry!

Hello Guys! I know I haven't posted in a while, but I have freaking writers block! I've started on the next chapter and I have a few ideas, but I'm just not happy with it! It's hard 'cause with the number of Daleks I have in the story you'd think everybody would be dead almost instantly, but it's a ship FULL of Timelords, and the Doctor takes on all the Daleks all the time and this is a whole ship of just that and his sister who currently, basically has the mind of a TARDIS. I'm not sure what to do. If you have any ideas, please, please, please(x infinity(instantly my mind thinks when I see this, 'to infinity and beyond!', thanks Toy Story)) review! I wouldn't mind if it's the silliest idea ever! I just need ideas! Thank you! XD


End file.
